X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=help%2Fhelp%2FhelpTOC.xml;h=a9b978898bacb2aeeef0866422e12b89bb9bbfb1;hb=a7818bc128f2dd28fbbde47b938266691fac1063;hp=5374e1a6b9627bad05b60f5d49469fa48a231799;hpb=076ec2ac8a7b1488476454c36b6a23255bed1529;p=jalview.git

diff --git a/help/help/helpTOC.xml b/help/help/helpTOC.xml
index 5374e1a..a9b9788 100755
--- a/help/help/helpTOC.xml
+++ b/help/help/helpTOC.xml
@@ -24,9 +24,12 @@
 	<tocitem text="Jalview Documentation" target="home" expand="true">
 			<tocitem text="What's new" target="new" expand="true">
 				<tocitem text="Latest Release Notes" target="release"/>
-				<tocitem text="VCF Variant Attributes" target="importvcf.attribs"/>
-				<tocitem text="Feature Filters and Attribute Colourschemes" target="features.featureschemes" />
-				
+        		<tocitem text="Support for ChimeraX" target="chimera"/>
+				<tocitem text="Support for Pymol" target="pymol"/>
+				<tocitem text="Structures via 3D Beacons" target="structuresvia3dbeacons" />
+				<tocitem text="Startup Memory Settings" target="startupprefs" />
+		        <tocitem text="The Java Console, Logging and Reporting Bugs" target="logging" />
+		        <tocitem text="Command line launch scripts" target="jalviewcltool"/>
 		</tocitem>
 		
 		<tocitem text="Editing Alignments" target="edit" />
@@ -62,6 +65,7 @@
 			<tocitem text="Feature Colourschemes" target="features.featureschemes" />
 			<tocitem text="User Defined Sequence Features" target="seqfeatcreat" />
 			<tocitem text="Editing Sequence Features" target="seqfeatedit" />
+			<tocitem text="HTML Feature Attributes report" target="seqfeatures.report" />
 			<tocitem text="HTML annotation report" target="io.seqreport" />
 		</tocitem>
 		
@@ -129,9 +133,10 @@
 		</tocitem>
 		<tocitem text="3D Structure Data" target="viewingpdbs" expand="false">
 			<tocitem text="PDB Sequence Fetcher" target="pdbfetcher" />
-			<tocitem text="PDB Structure Chooser" target="pdbchooser" />
+			<tocitem text="PDB &amp; 3D-Beacons Structure Chooser" target="pdbchooser" />
 			<tocitem text="Jmol Viewer" target="pdbjmol" />
-			<tocitem text="Chimera Viewer" target="chimera" />			
+			<tocitem text="Chimera/X Viewer" target="chimera" />
+			<tocitem text="Pymol Viewer" target="pymol" />			
 		</tocitem>
 		<tocitem text="Viewing RNA structures" target="varna" expand="false"/>
 		<tocitem text="Opening URLs from Jalview" target="urllinks" expand="true">
@@ -154,6 +159,7 @@
 			</tocitem>
 		</tocitem>
 		<tocitem text="Preferences" target="preferences" />
+    <tocitem text="The Java Console, Logging and Reporting Bugs" target="logging" />
 		<tocitem text="Scripting with Groovy" target="groovy">
 			<tocitem text="Groovy Features Counter example" target="groovy.featurescounter"/>
 		</tocitem>